SMTL ID : 5c4w.2 (3 other biounits)

Crystal structure of coxsackievirus A16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 13 residues within 4Å: Chain A: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, V.179, M.195, Y.201, W.203, N.228, M.230 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.111, A:L.113, A:F.135, A:F.137, A:Y.155, A:Y.155, A:V.179, A:W.203, A:N.228 Hydrogen bonds: A:L.113 SPH.10: 13 residues within 4Å: Chain E: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, V.179, M.195, Y.201, W.203, N.228, M.230 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:I.111, E:L.113, E:F.135, E:F.137, E:Y.155, E:Y.155, E:V.179, E:W.203, E:N.228 Hydrogen bonds: E:L.113 SPH.19: 13 residues within 4Å: Chain I: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, V.179, M.195, Y.201, W.203, N.228, M.230 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:I.111, I:L.113, I:F.135, I:F.137, I:Y.155, I:Y.155, I:V.179, I:W.203, I:N.228 Hydrogen bonds: I:L.113 SPH.28: 13 residues within 4Å: Chain M: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, V.179, M.195, Y.201, W.203, N.228, M.230 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:I.111, M:L.113, M:F.135, M:F.137, M:Y.155, M:Y.155, M:V.179, M:W.203, M:N.228 Hydrogen bonds: M:L.113 SPH.37: 13 residues within 4Å: Chain Q: I.111, D.112, L.113, M.114, F.135, F.137, Y.155, V.179, M.195, Y.201, W.203, N.228, M.230 10 PLIP interactions: 10 interactions with chain Q Hydrophobic interactions: Q:I.111, Q:L.113, Q:F.135, Q:F.137, Q:Y.155, Q:Y.155, Q:V.179, Q:W.203, Q:N.228 Hydrogen bonds: Q:L.113

10 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: T.28, A.29, N.31, N.71 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.28, A:A.29 K.5: 6 residues within 4Å: Chain A: Q.189 Chain C: V.20, S.21 Chain G: P.8 Chain K: E.5 Chain O: G.1 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:P.8 K.11: 4 residues within 4Å: Chain E: T.28, A.29, N.31, N.71 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.28, E:A.29 K.14: 6 residues within 4Å: Chain E: Q.189 Chain G: V.20, S.21 Chain K: P.8 Chain O: E.5 Chain S: G.1 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:P.8 K.20: 4 residues within 4Å: Chain I: T.28, A.29, N.31, N.71 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.28, I:A.29 K.23: 6 residues within 4Å: Chain C: G.1 Chain I: Q.189 Chain K: V.20, S.21 Chain O: P.8 Chain S: E.5 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:P.8 K.29: 4 residues within 4Å: Chain M: T.28, A.29, N.31, N.71 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.28, M:A.29 K.32: 6 residues within 4Å: Chain C: E.5 Chain G: G.1 Chain M: Q.189 Chain O: V.20, S.21 Chain S: P.8 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:P.8 K.38: 4 residues within 4Å: Chain Q: T.28, A.29, N.31, N.71 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:T.28, Q:A.29 K.41: 6 residues within 4Å: Chain C: P.8 Chain G: E.5 Chain K: G.1 Chain Q: Q.189 Chain S: V.20, S.21 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:P.8

5 x NA: SODIUM ION(Non-functional Binders)

NA.3: 8 residues within 4Å: Chain A: V.44, P.45, L.47, Q.48 Chain D: H.62, E.63, A.65, P.67 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.62, A:Q.48 NA.12: 8 residues within 4Å: Chain E: V.44, P.45, L.47, Q.48 Chain H: H.62, E.63, A.65, P.67 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.44, E:Q.48 NA.21: 8 residues within 4Å: Chain I: V.44, P.45, L.47, Q.48 Chain L: H.62, E.63, A.65, P.67 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:E.63, I:Q.48 NA.30: 8 residues within 4Å: Chain M: V.44, P.45, L.47, Q.48 Chain P: H.62, E.63, A.65, P.67 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:Q.48, P:H.62 NA.39: 8 residues within 4Å: Chain Q: V.44, P.45, L.47, Q.48 Chain T: H.62, E.63, A.65, P.67 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain T Hydrogen bonds: Q:Q.48, T:E.63

25 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.236 Chain E: R.250 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: H.162, P.163, Y.164 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain C: D.89, P.90, G.91, R.92, W.111, H.180, A.181 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain C: G.1 Chain K: G.19, V.20 Chain L: Y.32 Chain O: K.7 Chain S: P.3 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain C: G.27 Chain D: N.15, K.34 Chain E: Q.76, N.82 Chain H: R.43, Q.44 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain E: R.236 Chain I: R.250 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain F: H.162, P.163, Y.164 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain G: D.89, P.90, G.91, R.92, W.111, H.180, A.181 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: P.3 Chain G: G.1 Chain O: G.19, V.20 Chain P: Y.32 Chain S: K.7 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain G: G.27 Chain H: N.15, K.34 Chain I: Q.76, N.82 Chain L: R.43, Q.44 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain I: R.236 Chain M: R.250 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain J: H.162, P.163, Y.164 Ligand excluded by PLIP CL.25: 7 residues within 4Å: Chain K: D.89, P.90, G.91, R.92, W.111, H.180, A.181 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain C: K.7 Chain G: P.3 Chain K: G.1 Chain S: G.19, V.20 Chain T: Y.32 Ligand excluded by PLIP CL.27: 7 residues within 4Å: Chain K: G.27 Chain L: N.15, K.34 Chain M: Q.76, N.82 Chain P: R.43, Q.44 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain M: R.236 Chain Q: R.250 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain N: H.162, P.163, Y.164 Ligand excluded by PLIP CL.34: 7 residues within 4Å: Chain O: D.89, P.90, G.91, R.92, W.111, H.180, A.181 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain C: G.19, V.20 Chain D: Y.32 Chain G: K.7 Chain K: P.3 Chain O: G.1 Ligand excluded by PLIP CL.36: 7 residues within 4Å: Chain O: G.27 Chain P: N.15, K.34 Chain Q: Q.76, N.82 Chain T: R.43, Q.44 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain A: R.250 Chain Q: R.236 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain R: H.162, P.163, Y.164 Ligand excluded by PLIP CL.43: 7 residues within 4Å: Chain S: D.89, P.90, G.91, R.92, W.111, H.180, A.181 Ligand excluded by PLIP CL.44: 6 residues within 4Å: Chain G: G.19, V.20 Chain H: Y.32 Chain K: K.7 Chain O: P.3 Chain S: G.1 Ligand excluded by PLIP CL.45: 7 residues within 4Å: Chain A: Q.76, N.82 Chain D: R.43, Q.44 Chain S: G.27 Chain T: N.15, K.34 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity. J.Virol. (2015)

Release Date

2015-08-26

Peptides

VP1: AEIMQ
VP2: BFJNR
VP3: CGKOS
VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

VP1

VP2

VP3

VP4

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